InPlot: Integration Plot

In bioinfoDZ/RISC: Robust Integration of Single-Cell RNA-Seq Datasets

Integration Plot

Description

The "InPlot" function makes the plot to show how the PCs explain the variance for data integration. This plot helps the users to select the optimal reference and the PCs to perform data integration.

Usage

InPlot(
  object = NULL,
  var.gene = NULL,
  Colors = NULL,
  nPC = 20,
  neighbor = 30,
  res = 1,
  method = "louvain",
  algorithm = "kd_tree",
  ncore = 1,
  minPC = 11,
  Std.cut = 0.95,
  bin = 5
)

Arguments

object	A list of RISC objects.
var.gene	The highly variable genes.
Colors	The colors labeling for different data sets.
nPC	The PCs will be calculated.
neighbor	The nearest neighbors.
res	The resolution of cluster searched for, works in "louvain" method.
method	The method of cell clustering for individual datasets.
algorithm	The algorithm for knn, the default is "kd_tree", all options: "kd_tree", "cover_tree", "CR", "brute".
ncore	The number of multiple cores for testing.
minPC	The minimal PCs for detecting cell clustering.
Std.cut	The cutoff of standard deviation of the PCs.
bin	The bin number for calculating cell clustering.

References

Liu et al., Nature Biotech. (2021)

bioinfoDZ/RISC documentation built on March 30, 2024, 9:19 p.m.